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Author |
Rezaei, M.; Ghasemitarei, M.; Razzokov, J.; Yusupov, M.; Ghorbanalilu, M.; Ejtehadi, M.R. |
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Title |
In silico study of the impact of oxidation on pyruvate transmission across the hVDAC1 protein channel |
Type |
A1 Journal article |
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Year  |
2024 |
Publication |
Archives of biochemistry and biophysics |
Abbreviated Journal |
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Volume |
751 |
Issue |
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Pages |
109835-109837 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
The overexpression of voltage dependent anion channels (VDACs), particularly VDAC1, in cancer cells compared to normal cells, plays a crucial role in cancer cell metabolism, apoptosis regulation, and energy homeostasis. In this study, we used molecular dynamics (MD) simulations to investigate the effect of a low level of VDAC1 oxidation (induced e.g., by cold atmospheric plasma (CAP)) on the pyruvate (Pyr) uptake by VDAC1. Inhibiting Pyr uptake through VDAC1 can suppress cancer cell proliferation. Our primary target was to study the translocation of Pyr across the native and oxidized forms of hVDAC1, the human VDAC1. Specifically, we employed MD simulations to analyze the hVDAC1 structure by modifying certain cysteine residues to cysteic acids and methionine residues to methionine sulfoxides, which allowed us to investigate the effect of oxidation. Our results showed that the free energy barrier for Pyr translocation through the native and oxidized channel was approximately 4.3 +/- 0.7 kJ mol-1 and 10.8 +/- 1.8 kJ mol-1, respectively. An increase in barrier results in a decrease in rate of Pyr permeation through the oxidized channel. Thus, our results indicate that low levels of CAP oxidation reduce Pyr translocation, resulting in decreased cancer cell proliferation. Therefore, low levels of oxidation are likely sufficient to treat cancer cells given the inhibition of Pyr uptake. |
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Wos |
001127850500001 |
Publication Date |
2023-11-23 |
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ISSN |
0003-9861; 1096-0384 |
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Additional Links |
UA library record; WoS full record |
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Impact Factor |
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no |
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Call Number |
UA @ admin @ c:irua:202185 |
Serial |
9046 |
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Author |
Rezaei, M.; Sisakht, E.T.; Fazileh, F.; Aslani, Z.; Peeters, F.M. |
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Title |
Tight-binding model investigation of the biaxial strain induced topological phase transition in GeCH3 |
Type |
A1 Journal article |
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Year |
2017 |
Publication |
Physical review B |
Abbreviated Journal |
Phys Rev B |
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Volume |
96 |
Issue |
8 |
Pages |
085441 |
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Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
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Abstract |
We propose a tight-binding (TB) model, that includes spin-orbit coupling (SOC), to describe the electronic properties of methyl-substituted germanane (GeCH3). This model gives an electronic spectrum in agreement with first principle results close to the Fermi level. Using the Z(2) formalism, we show that a topological phase transition from a normal insulator (NI) to a quantum spin Hall (QSH) phase occurs at 11.6% biaxial tensile strain. The sensitivity of the electronic properties of this system on strain, in particular its transition to the topological insulating phase, makes it very attractive for applications in strain sensors and other microelectronic applications. |
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American Physical Society |
Place of Publication |
New York, N.Y |
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Wos |
000408570800004 |
Publication Date |
2017-08-29 |
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ISSN |
2469-9969; 2469-9950 |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
3.836 |
Times cited |
10 |
Open Access |
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Notes |
; ; |
Approved |
Most recent IF: 3.836 |
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Call Number |
UA @ lucian @ c:irua:145697 |
Serial |
4755 |
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Author |
Rezaei, M.; De Pue, J.; Seuntjens, P.; Joris, I.; Cornelis, W. |
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Title |
Quasi 3D modelling of vadose zone soil-water flow for optimizing irrigation strategies : challenges, uncertainties and efficiencies |
Type |
A1 Journal article |
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Year |
2017 |
Publication |
Environmental modelling and software |
Abbreviated Journal |
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Volume |
93 |
Issue |
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Pages |
59-77 |
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Keywords |
A1 Journal article; Sustainable Energy, Air and Water Technology (DuEL) |
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Abstract |
A quasi 3D modelling approach was developed by integrating a crop growth (LINGRA-N) and a hydrological model (Hydrus-1D) to simulate and visualize water flow, soil-water storage, water stress and crop yield over a heterogeneous sandy field. We assessed computational efficiency and uncertainty with low to high-spatial resolution input factors (soil-hydraulic properties, soil-layer thickness and groundwater level) and evaluated four irrigation scenarios (no, current, optimized and triggered) to find the optimal and cost-effective irrigation scheduling. Numerical results showed that the simulation uncertainty was reduced when using the high-resolution information while a fast performance was maintained. The approach accurately determined the field scale irrigation requirements, taking into account spatial variations of input information. Optimal irrigation scheduling is obtained by triggered-irrigation resulting in saving up to similar to 300% water as compared to the current-irrigation, while yield increased similar to 1%. Overall, the approach can be useful to help decision makers and applicants in precision farming. (C) 2017 Published by Elsevier Ltd. |
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Wos |
000403512500005 |
Publication Date |
2017-03-21 |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
1364-8152 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
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Times cited |
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Open Access |
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no |
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Call Number |
UA @ admin @ c:irua:144167 |
Serial |
8445 |
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Author |
Rezaei, M.; Seuntjens, P.; Joris, I.; Boenne, W.; Van Hoey, S.; Campling, P.; Cornelis, W.M. |
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Title |
Sensitivity of water stress in a two-layered sandy grassland soil to variations in groundwater depth and soil hydraulic parameters |
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A1 Journal article |
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Year |
2016 |
Publication |
Hydrology and earth system sciences |
Abbreviated Journal |
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Volume |
20 |
Issue |
1 |
Pages |
487-503 |
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Keywords |
A1 Journal article; Sustainable Energy, Air and Water Technology (DuEL) |
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Abstract |
Monitoring and modelling tools may improve irrigation strategies in precision agriculture. We used non-invasive soil moisture monitoring, a crop growth and a soil hydrological model to predict soil water content fluctuations and crop yield in a heterogeneous sandy grassland soil under supplementary irrigation. The sensitivity of the soil hydrological model to hydraulic parameters, water stress, crop yield and lower boundary conditions was assessed after integrating models. Free drainage and incremental constant head conditions were implemented in a lower boundary sensitivity analysis. A time-dependent sensitivity analysis of the hydraulic parameters showed that changes in soil water content are mainly affected by the soil saturated hydraulic conductivity K-s and the Mualem-van Genuchten retention curve shape parameters n and alpha. Results further showed that different parameter optimization strategies (two-, three-, four- or six-parameter optimizations) did not affect the calculated water stress and water content as significantly as does the bottom boundary. In this case, a two-parameter scenario, where K-s was optimized for each layer under the condition of a constant groundwater depth at 135-140 cm, performed best. A larger yield reduction, and a larger number and longer duration of stress conditions occurred in the free drainage condition as compared to constant boundary conditions. Numerical results showed that optimal irrigation scheduling using the aforementioned water stress calculations can save up to 12-22 % irrigation water as compared to the current irrigation regime. This resulted in a yield increase of 4.5-6.5 %, simulated by the crop growth model. |
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Wos |
000369668400028 |
Publication Date |
2016-01-29 |
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Abbreviated Series Title |
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Series Volume |
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Edition |
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ISSN |
1027-5606; 1607-7938 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
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Times cited |
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Open Access |
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Notes |
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no |
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Call Number |
UA @ admin @ c:irua:132259 |
Serial |
8514 |
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Author |
Rezaei, M.; Saey, T.; Seuntjens, P.; Joris, I.; Boenne, W.; Van Meirvenne, M.; Cornelis, W. |
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Title |
Predicting saturated hydraulic conductivity in a sandy grassland using proximally sensed apparent electrical conductivity |
Type |
A1 Journal article |
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Year |
2016 |
Publication |
Journal of applied geophysics |
Abbreviated Journal |
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Volume |
126 |
Issue |
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Pages |
35-41 |
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Keywords |
A1 Journal article; Sustainable Energy, Air and Water Technology (DuEL) |
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Abstract |
Finding a correspondence between soil hydraulic properties, such as saturated hydraulic conductivity (Ks) and apparent electrical conductivity (ECa) as an easily measurable parameter, may be a way forward to estimate the spatial distribution of hydraulic properties at the field scale. In this study, the spatial distributions of Ks, of soil ECa measured by a DUALEM-21S sensor and of soil physical properties were investigated in a sandy grassland. To predict field scale Ks, the statistical relationship between co-located soil Ks, and EMI-ECa was evaluated. Results demonstrated the large spatial variability of all studied properties with Ks being the most variable one (CV = 86.21%) followed by ECa (CV >= 53.77%). A significant negative correlation was found between In-transformed Ks and ECa (r = 0.83; P <= 0.01) at two depths of exploration (0-50 and 0-100 cm). This site specific relation between In Ks and ECa was used to predict saturated hydraulic conductivity over 0-50 cm depth for the whole field. The empirical relation was validated using an independent dataset of measured Ks. The statistical results demonstrate the robustness of this empirical relation with mean estimation error MEE = 0.46 (cm h(-1)), root-mean-square estimation errors RMSEE = 0.74 (cm h(-1)), coefficient of determination r(2) = 0.67 and coefficient of model efficiency Ce = 0.64. The relationship was then used to produce a detailed map of Ks for the whole field. The result will allow model predictions of spatially distributed water content in view of irrigation management. (C) 2016 Elsevier B.V. All rights reserved. |
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Wos |
000371361200004 |
Publication Date |
2016-01-17 |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0926-9851 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
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Times cited |
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Open Access |
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Notes |
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Approved |
no |
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Call Number |
UA @ admin @ c:irua:132349 |
Serial |
8403 |
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Author |
Rezaei, M.; Seuntjens, P.; Shahidi, R.; Joris, I.; Boenne, W.; Al-Barri, B.; Cornelis, W. |
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Title |
The relevance of in-situ and laboratory characterization of sandy soil hydraulic properties for soil water simulations |
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A1 Journal article |
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Year |
2016 |
Publication |
Journal of hydrology |
Abbreviated Journal |
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Volume |
534 |
Issue |
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Pages |
251-265 |
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Keywords |
A1 Journal article; Sustainable Energy, Air and Water Technology (DuEL) |
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Abstract |
Field water flow processes can be precisely delineated with proper sets of soil hydraulic properties derived from in situ and/or laboratory experiments. In this study we analyzed and compared soil hydraulic properties obtained by traditional laboratory experiments and inverse optimization tension infiltrometer data along the vertical direction within two typical Podzol profiles with sand texture in a potato field. The main goal was to identify proper sets of hydraulic parameters and to evaluate their relevance on hydrological model performance for irrigation management purposes. Tension disc infiltration experiments were carried out at four and five different depths for both profiles at consecutive negative pressure heads of 12, 6, 3 and 0.1 cm. At the same locations and depths undisturbed samples were taken to determine Mualem-van Genuchten (MVG) hydraulic parameters (theta(r), residual water content, theta(s), saturated water content, alpha and n, shape parameters and K-ls, saturated hydraulic conductivity) in the laboratory. Results demonstrated horizontal differences and vertical variability of hydraulic properties. The tension disc infiltration data fitted well in inverse modeling using Hydrus 2D/3D in combination with final water content at the end of the experiment, theta(f). Four MVG parameters (theta(s), alpha, n and field saturated hydraulic conductivity K-fs) were estimated (theta(r) set to zero), with estimated K-ls and alpha values being relatively similar to values from Wooding's solution which used as initial value and estimated theta(s) corresponded to (effective) field saturated water content, theta(f). The laboratory measurement of K-ls yielded 2-30 times higher values than the field method K-fs from top to subsoil layers, while there was a significant correlation between both K-s values (r = 0.75). We found significant differences of MVG parameters theta(s), n and alpha values between laboratory and field measurements, but again a significant correlation was observed between laboratory and field MVG parameters namely K-s, n, theta(s) (r >= 0.59). Assessment of the parameter relevance in 1-D model simulations, illustrated that the model over predicted and under predicted top soil-water content using laboratory and field experiments data sets respectively. The field MVG parameter data set resulted in better agreement to observed soil-water content as compared to the laboratory data set at nodes 10 and 20 cm. However, better simulation results were achieved using the laboratory data set at 30-60 cm depths. Results of our study do not confirm whether laboratory or field experiments data sets are most appropriate to predict soil water fluctuations in a complete soil profile, while field experiments are preferred in many studies. (C) 2016 Elsevier B.V. All rights reserved. |
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Wos |
000371940900022 |
Publication Date |
2016-01-11 |
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Abbreviated Series Title |
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Series Issue |
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Edition |
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ISSN |
0022-1694 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
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Times cited |
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Open Access |
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Notes |
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Approved |
no |
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Call Number |
UA @ admin @ c:irua:133161 |
Serial |
8657 |
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Author |
Borhani, A.H.; Berghmans, H.; Trashin, S.; De Wael, K.; Fago, A.; Moens, L.; Habibi-Rezaei, M.; Dewilde, S. |
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Title |
Kinetic properties and heme pocket structure of two domains of the polymeric hemoglobin of Artemia in comparison with the native molecule |
Type |
A1 Journal article |
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Year |
2015 |
Publication |
Biochimica et biophysica acta : proteins and proteomics |
Abbreviated Journal |
Bba-Proteins Proteom |
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Volume |
1854 |
Issue |
10a |
Pages |
1307-1316 |
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Keywords |
A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation) |
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Abstract |
In this project, we studied some physicochemical properties of two different globin domains of the polymeric hemoglobin of the brine shrimp Artemia salina and compared them with those of the native molecule. Two domains (AsHbC1D1 and AsHbC1D5) were cloned and expressed in BL21(DE3)pLysS strain of Escherichiacoli. The recombinant proteins as well as the native hemoglobin (AfHb) were purified from bacteria and frozen Artemia, respectively by standard chromatographic methods and assessed by SDS-PAGE. The heme environment of these proteins was studied by optical spectroscopy and ligand-binding kinetics (e.g. CO association and O2 binding affinity) were measured for the two recombinant proteins and the native hemoglobin. This indicates that the CO association rate for AsHbC1D1 is higher than that of AsHbC1D5 and AfHb, while the calculated P50 value for AsHbC1D1 is lower than that of AsHbC1D5 and AfHb. The geminate and bimolecular rebinding parameters indicate a significant difference between both domains. Moreover, EPR results showed that the heme pocket in AfHb is in a more closed conformation than the heme pocket in myoglobin. Finally, the reduction potential of − 0.13 V versus the standard hydrogen electrode was determined for AfHb by direct electrochemical measurements. It is about 0.06 V higher than the potential of the single domain AsHbC1D5. This work shows that each domain in the hemoglobin of Artemia has different characteristics of ligand binding. |
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Wos |
000362307500008 |
Publication Date |
2015-05-22 |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
1570-9639 |
ISBN |
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Additional Links |
UA library record; WoS full record |
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Impact Factor |
2.773 |
Times cited |
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Open Access |
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Notes |
; This work was supported by the general grant for visiting scholar of the Ministry of Science, Research and Technology of I. R. Iran and by the University of Antwerp. ; |
Approved |
Most recent IF: 2.773; 2015 IF: 2.747 |
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Call Number |
UA @ admin @ c:irua:125909 |
Serial |
5683 |
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